Additional file 1:
Format: PDF Size 137KB
Table S1 Comparison of wild barley 454 transcripts and Hv fl-cDNA sequences against different plant genomes.
Barley data(No. of sequences) / 1Genome Annotation / One-to-many / RBH
No. of PUTs / % of PUTs / No. of PUTs / %of PUTs
B1K2
(20,439) / Barley / 13402 / 65.6 / 10151 / 49.7
Brachypodium / 10788 / 52.8 / 7203 / 35.2
Rice / 9423 / 46.1 / 6217 / 30.4
Sorghum / 8799 / 43.1 / 5768 / 28.2
Maize / 8297 / 40.6 / 4953 / 24.2
Arabidopsis / 3386 / 16.6 / 1703 / 8.3
B1K30
(21,494) / Barley / 13632 / 63.4 / 9996 / 46.5
Brachypodium / 10545 / 49.1 / 6976 / 32.5
Rice / 9181 / 42.7 / 6048 / 28.1
Sorghum / 8584 / 39.9 / 5613 / 26.1
Maize / 8108 / 37.7 / 4765 / 22.2
Arabidopsis / 3323 / 15.5 / 1646 / 7.7
B1K
(28,719) / Barley / 17033 / 59.3 / 11859 / 41.3
Brachypodium / 13404 / 46.7 / 8246 / 28.7
rice / 11649 / 40.6 / 7158 / 24.9
sorghum / 10835 / 37.7 / 6613 / 23.0
Hv fl-cDNA (23,356) / Brachypodium / 15237 / 65.2 / 9578 / 41.0
rice / 13073 / 56.0 / 3770 / 16.1
sorghum / 12125 / 51.9 / 7013 / 30.0
maize / 10193 / 43.6 / 7438 / 31.8
Arabidopsis / 2907 / 12.4 / 1659 / 7.1
1Genome Annotation and database version (# of protein sequences): Barley HighConf genes MIPS 23Mar12 CDS (26,159), Brachypodium distachyon v1.2 (31,029), Rice MUS6 (68,619), Sorghum-filtered v1.4 (35,899), Maize-filtered ZmB73-4a.53 (53,764), and Arabidopsis thaliana TAIR10.3 (35,386). MegaBLAST cutoff: ≤1e-10, ³ 75 %ID & ³ 50 nt, and BLASTX cutoff: ≤1e-6 ³ 75 %ID & ³ 33 aa
Table S4 Summary of stress-related candidate genes identified from functional annotation of B1K2 and B1K30 transcriptome sequences.
Candidate genes / B1K2 PUTs / B1K30 PUtsABC transporter / 104 / 93
ABRE / 4 / 4
Aldehyde dehydrogenase / 22 / 20
Amino acid transport protein (AAP2) / 4 / -
AP2 / 10 / 9
Aquaporin / 16 / 10
Betaine aldehyde dehydrogenase / 10 / 4
bHLH / 19 / 21
bZIP / 16 / 14
Calmodulin / 39 / 40
CBF / 3 / 4
CDPK / 17 / 17
Dehydrin / - / 1
DREB / 1 / 2
ERD / 1 / 1
ERF / 5 / 2
Histone deacetylase / 17 / 17
Homeodomain / 10 / 11
HSF / 11 / 12
HSP / 61 / 63
MAPK / 28 / 19
MYB / 46 / 42
MYC / 1 / 3
NAC / 9 / 11
NADP / 46 / 45
PEPC / 20 / 14
Phospholipase / 23 / 38
Polyamines / 20 / 22
Proline / 25 / 32
Pyruvate dehydrogenase / 21 / 19
Stress responsive / 7 / 8
SUMO / 10 / 12
Superoxide dismutase / 7 / 8
Trehalose / 10 / 10
WRKY / 11 / 12
Zinc finger / 185 / 241
Total abiotic stress-related 454 transcripts / 839 / 881
ABRE, ABA-responsive element; AP2, activator protein-2 ; bHLH, basic helix-loop-helix; bZIP, basic leucine zipper domain; CBF, C-repeat biding factor; CDPK, calcium-dependent protein kinase; DRE, dehydration-responsive element; HSF, heat shock factor; HSP, heat shock protein; MAPK, mitogen activated protein kinase; NAC, nascent polypeptide-associated complex; PEPC, phosphoenolpyruvate carboxylase; Polyamine (polyamine oxidase, S-adenosylmethionine, S-adenosylmethionine decarboxylase, S-adenosylmethionine synthase, spermidine, spermidine synthase, spermine and spermine synthase); SUMO, small ubiquitin-related modifier; Trehalase (trehalase, trehalose-phosphatase and trehalase-phosphate synthase).
Table S5 CDS predicted from assembled unique transcripts based on comparison against Hv. HC CDS and usinf OrfPredictor.
B1K2 (%) / B1K30 (%) / B1K (%)Total clustered unique transcripts / 20,439 / 21,492 / 28,720
CDS predicted based on one-to-many hits (≥ 50 bp):
· Unique transcripts homologous to Hv. HC CDS / 13,402 (65.6) / 13,632 (63.4) / 17,033 (59.3)
· Hv. HC CDS homologous to unique transcripts / 11,497 (44.0) / 11,266 (43.1) / 13,211 (50.5)
CDS predicted based on RBH (≥ 50 bp):
· Unique transcripts homologous to Hv. HC CDS / 10,151 (49.7) / 9,996 (46.5) / 11,859 (41.3)
· Hv. HC CDS homologous to unique transcripts / 10,660 (40.8) / 10,497 (40.1) / 12,226 (46.7)
CDS predicted based on BLASTX hit (≥ 70 bp):
· Unique transcripts homologous to Hv. HC CDS / 13,722 (67.1) / 13,688 (63.7) / 17,675 (61.5)
· Hv. HC CDS homologous to unique transcripts / 10,129 (38.7) / 9,871 (37.8) / 11,735 (44.9)
· CDS fully covered (100% of Hv. HC CDS) / 597 (2.9) / 488 (2.3) / 796 (2.8)
· CDS ≥ 90% of Hv. HC CDS / 984 (4.8) / 754 (3.5) / 1,328 (4.6)
· CDS ≥ 85% of Hv. HC CDS / 1,188 (5.8) / 926 (4.3) / 1,630 (5.7)
· Unique transcripts without hit in Hv. HC genes / 6,717 (32.9) / 7,804 (36.3) / 11,045 (38.5)
CDS predicted by OrfPredictor
· Unique transcripts with CDS / 20,348 (99.6) / 21,397 (99.6) / 28,549 (99.4)
· With CDS & homolog to Hv. HC genes / 13,722 / 13,684 / 17,604
· With CDS but not homolog to Hv. HC genes / 6,626 / 7,713 / 10,945
· Without CDS but homolog to Hv. HC genes / 0 / 2 / 71
· Mean CDS length (bp) / 357 / 321 / 350
· CDS ≥ 100 bp / 19,700 (96.8) / 20,597 (96.3) / 27,324 (95.7)
· CDS ≥ 500 bp / 3,895 (19.1) / 3,319 (15.6) / 5,530 (19.4)
· CDS ≥ 1 kb / 721 (3.5) / 469 (2.1) / 1,146 (4.0)
· CDS ≥ 85% of Hv. HC CDS / 1,112 (8.1) / 897 (6.6) / 1,512 (8.6)
· CDS equal with Hv. HC CDS / 449 (3.3) / 344 (2.5) / 584 (3.3)
· CDS longer than Hv. HC CDS / 320 (2.3) / 286 (2.1) / 456 (2.6)
CDS predicted from novel transcripts / 3,245 / 3,674 / 7,102
· Novel transcripts with predicted CDS / 3,174 (98.7) / 3,600 (98.0) / 6,953 (97.9)
· CDS ≥ 100 bp / 2,774 (85.5) / 3,128 (85.1) / 6,045 (85.1)
· CDS ≥ 200 bp / 1,031 (31.8) / 998 (27.2) / 2,099 (29.6)
· CDS ≥ 500 bp / 19 (0.6) / 15 (0.4) / 38 (0.5)
Table S6 Summary of SNPs shared among three wild barley ecotypes.
Reference (Morex) vs. / Private and shared SNPs: / Remarkin number / in %
B1K2 / 20741 / 52.45 / B1K2-specific SNPs
B1K2 vs. B1K30 / 9029 / 22.83 / SNPs found in both B1K2 & B1k30
B1K2 vs. B1K4* / 5444 / 13.77 / SNPs found in both B1K2 & B1K4
B1K2 vs. B1K30 vs. B1K4 / 4331 / 10.95 / SNPs found in all three ecotypes
B1K2 total SNPs / 39545
B1K30 / 18311 / 50.83 / B1K30-specific SNPs
B1K30 vs. B1K2 / 9029 / 25.07 / SNPs found in both B1K30 & B1K2
B1K30 vs. B1K4 / 4351 / 12.08 / SNPs found in both B1K30 & B1K2
B1K30 vs. B1K2 vs. B1K4 / 4331 / 12.02 / SNPs found in all three ecotypes
B1K30 total SNPs / 36022
*B1K4: SNPs data from wild barley ecotype used for barley genome sequencing project.
Table S7 List of top 30 barley genes with high number of SNP with moderate and high effects (nsSNP+). Top 30 genes were selected based on nsSNP+ in B1K2.
Gene / Chr. / B1K2 / B1K30 / nsSNP+:sSNP / DescriptionsSNP / nsSNP+ / sSNP / nsSNP+ / B1K2 / B1K30
MLOC_62296 / 5 / 10 / 35 / 4 / 14 / 3.50 / 3.50 / Unknown protein
MLOC_54762 / 2 / 57 / 25 / 13 / 3 / 0.44 / 0.23 / Chloride channel 1
MLOC_7441 / 3 / 10 / 23 / 0 / 1 / 2.30 / Trimeric LpxA-like
MLOC_65275 / 3 / 39 / 22 / 23 / 13 / 0.56 / 0.57 / Nup98 protein/Peptidase S59, nucleoporin
MLOC_37095 / 5 / 88 / 20 / 16 / 1 / 0.23 / 0.06 / Ubiquitin-activating enzyme/NAD(P)-binding domain
MLOC_55424 / 4 / 34 / 19 / 0 / 4 / 0.56 / 60S acidic ribosomal protein P0, putative, expressed
MLOC_73609 / 5 / 14 / 19 / 14 / 19 / 1.36 / 1.36 / Saposin B domain-containing protein
MLOC_59407 / 3 / 35 / 18 / 9 / 9 / 0.51 / 1.00 / Vacuolar processing enzyme 3
MLOC_59273 / 1 / 14 / 17 / 13 / 10 / 1.21 / 0.77 / Ribosomal protein L28e
MLOC_81109 / 1 / 36 / 17 / 23 / 12 / 0.47 / 0.52 / Chlorophyll a-b binding protein 3C-like
MLOC_34629 / 4 / 20 / 15 / 10 / 8 / 0.75 / 0.80 / O-methyltransferase
MLOC_77452 / 3 / 8 / 15 / 1.88 / Unknown protein
MLOC_17849 / 4 / 6 / 14 / 2.33 / Peptidyl-prolyl cis-trans isomerase
MLOC_44284 / 4 / 14 / 13 / 0.93 / Kinase interacting (KIP1-like) protein
MLOC_54382 / 1 / 117 / 13 / 68 / 10 / 0.11 / 0.15 / Actin
MLOC_56003 / 1 / 53 / 13 / 32 / 7 / 0.25 / 0.22 / Actin
MLOC_77535 / 2 / 10 / 12 / 3 / 2 / 1.20 / 0.67
MLOC_18287 / 5 / 6 / 11 / 9 / 17 / 1.83 / 1.89 / Pore-forming toxin-like protein Hfr-2
MLOC_37976 / 3 / 11 / 10 / 0.91 / Beta glucosidase like protein
MLOC_6795 / 4 / 14 / 9 / 1 / 0 / 0.64 / 0.00 / Methyltransferase type 11
MLOC_69295 / 5 / 14 / 9 / 3 / 0 / 0.64 / 0.00 / Ferritin
MLOC_9887 / 2 / 16 / 8 / 0.50 / Bifunctional inhibitor/lipid-transfer, seed storage 2S albumin superfamily protein
MLOC_15685 / 6 / 16 / 7 / 5 / 1 / 0.44 / 0.20 / GOLD
MLOC_49652 / 2 / 8 / 7 / 0.88 / General substrate transporter/Sugar transporter
MLOC_67053 / 3 / 19 / 7 / 0.37 / Helix-loop-helix DNA-binding
MLOC_7780 / 1 / 17 / 7 / 4 / 2 / 0.41 / 0.50 / Malate dehydrogenase
MLOC_10713 / 3 / 12 / 6 / 13 / 6 / 0.50 / 0.46 / small ubiquitin-like modifier 1
MLOC_10832 / 3 / 5 / 6 / 1.20 / THO complex subunit
MLOC_360 / 5 / 33 / 6 / 38 / 4 / 0.18 / 0.11 / Elongation factor 2
MLOC_37449 / 5 / 22 / 6 / 0.27 / Heat shock protein